I’ve used Venn to generate the overview I am looking for in comparing groups. But now I want to know not just the number of unique sequences in each group as well as the overlap, but their identity. How can I get the actual sequence/OTU name for each of these (unique in each group as well as overlap)? I know from the documentation that get.sharedseqs is supposed to do this for me, but I’m having a hard time figuring out the exact command parameters. I have the .shared file for the entire dataset, and I know how to make a groups file, but the command requires a .list file - I’ve been following the MiSEQ protocol but am not sure which command is used to generate the appropriate .list file. Is it just the list file that was created by the clustering? For MiSEQ this is stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.an.unique_list.list - yes? And that will let me find OTU/species in common between two groups? And then, how do I find the ones not shared?
UPDATE: I ran VENN and it gives me the list of SHARED OTU’s. But not the ones that are unique. It would be nice if there was an option, if doing a pairwise venn comparison, to get the non-shared ones as well…
Thanks for any help you can provide…